Several countries in Africa have changed their first-line treatment for uncomplicated malaria to an ACT. Burkina Faso has changed its policy to Artemether-Lumefantrine (AL) and Artesunate-Amodiaquine (AQ+AS). However, such choice has been done without knowing the local effectiveness of these drugs when they are given to patients in real life conditions, without direct observation of the drug administration. Thus, this study aims at investigating the effectiveness of AQ+AS and AL, when given to children with uncomplicated malaria in Burkina Faso.